title: High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake.
abstract: Deep Lake in Antarctica is a globally isolated, hypersaline system that remains liquid at temperatures down to -20 °C. By analyzing metagenome data and genomes of four isolates we assessed genome variation and patterns of gene exchange to learn how the lake community evolved. The lake is completely and uniformly dominated by haloarchaea, comprising a hierarchically structured, low-complexity community that differs greatly to temperate and tropical hypersaline environments. The four Deep Lake isolates represent distinct genera (∼85% 16S rRNA gene similarity and ∼73% genome average nucleotide identity) with genomic characteristics indicative of niche adaptation, and collectively account for ∼72% of the cellular community. Network analysis revealed a remarkable level of intergenera gene exchange, including the sharing of long contiguous regions (up to 35 kb) of high identity (∼100%). Although the genomes of closely related Halobacterium, Haloquadratum, and Haloarcula (>90% average nucleotide identity) shared regions of high identity between species or strains, the four Deep Lake isolates were the only distantly related haloarchaea to share long high-identity regions. Moreover, the Deep Lake high-identity regions did not match to any other hypersaline environment metagenome data. The most abundant species, tADL, appears to play a central role in the exchange of insertion sequences, but not the exchange of high-identity regions. The genomic characteristics of the four haloarchaea are consistent with a lake ecosystem that sustains a high level of intergenera gene exchange while selecting for ecotypes that maintain sympatric speciation. The peculiarities of this polar system restrict which species can grow and provide a tempo and mode for accentuating gene exchange.
authors.affiliation: School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia.
authors.forename: Matthew Z
authors.initials: MZ
authors.lastname: DeMaere
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Williams
authors.forename: Michelle A
authors.initials: MA
authors.lastname: Allen
authors.forename: Mark V
authors.initials: MV
authors.lastname: Brown
authors.forename: John A E
authors.initials: JA
authors.lastname: Gibson
authors.forename: John
authors.initials: J
authors.lastname: Rich
authors.forename: Federico M
authors.initials: FM
authors.lastname: Lauro
authors.forename: Michael
authors.initials: M
authors.lastname: Dyall-Smith
authors.forename: Karen W
authors.initials: KW
authors.lastname: Davenport
authors.forename: Tanja
authors.initials: T
authors.lastname: Woyke
authors.forename: Nikos C
authors.initials: NC
authors.lastname: Kyrpides
authors.forename: Susannah G
authors.initials: SG
authors.lastname: Tringe
authors.forename: Ricardo
authors.initials: R
authors.lastname: Cavicchioli
mesh_terms: D000864:Antarctic Regions; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D020745:Genome, Archaeal / Q000502:physiology*; D006216:Halobacteriaceae / Q000235:genetics*; D060106:Lakes / Q000382:microbiology*; D054892:Metagenome; D019642:RNA, Archaeal / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D014871:Water Microbiology
chemical_list: D019642:RNA, Archaeal; D012336:RNA, Ribosomal, 16S
keywords: Antarctic haloarchaea; BJ1 virus; fragment recruitment; mobile genetic elements; saltern